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=== Rmpi === <!--T:16--> | |||
====Installing==== | |||
Below is the procedure to install [https://cran.r-project.org/web/packages/Rmpi/index.html Rmpi], an interface (wrapper) to MPI routines, which allow R to run in parallel. | Below is the procedure to install [https://cran.r-project.org/web/packages/Rmpi/index.html Rmpi], an interface (wrapper) to MPI routines, which allow R to run in parallel. | ||
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This will use the default version of MPI to perform the install, which is currently 2.1.1. | This will use the default version of MPI to perform the install, which is currently 2.1.1. | ||
====Running==== | |||
Please your R code in a script file, in this case mpi_test.R. | |||
Give the file executable permissions with: | |||
chmod u+x rmpi_test.R | |||
Then place the following in a job submission script, job.sh : | |||
#!/bin/bash | |||
#SBATCH --account=def-ppomorsk | |||
#SBATCH --ntasks=4 # number of MPI processes | |||
#SBATCH --mem-per-cpu=1024M # memory; default unit is megabytes | |||
#SBATCH --time=0-01:00 # time (DD-HH:MM) | |||
module load r/3.4.0 | |||
export R_LIBS=~/local/R_libs/ | |||
srun Rscript rmpi_test.R | |||
Finally, submit the job with: | |||
sbatch job.sh | |||
For more on submitting jobs, see the [https://docs.computecanada.ca/wiki/Running_jobs#MPI_job Running jobs] page. | |||
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